[BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb

[Hilmar Lapp]

On Sep 3, 2008, at 9:10 PM, Nick Matzke wrote:

> Do you know of a way to get sudo to read the standard environmental  
> variables or something like that?


You can put them in the shell initialization files of the target user  
(root in your examples).

Note that sudo will remove the PERL5LIB, PERLLIB, and PERLOPT  
environment variables when invoked, so as it turns out that invoking  
perl w/ and w/o sudo isn't the same is actually by design if you have  
have PERL5LIB changed for your local user.

In reality there should rarely if ever be a need to use sudo when  
running a biosql, bioperl-db, or bioperl perl script. Are you sure you  
need to do this?

The reason you saw the problems were most likely because the  
directory /<your ActiveState install path>/Bundle was in PERL5LIB, and  
was so relatively at the front. I doubt that it needs to be there to  
begin with; have you observed any failures or problems if you remove  
that directory completely?

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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